NEW YORK (CBSNewYork/AP) — There was overcrowding and confusion on several commuter rail lines as millions of people tried to make their way into and out of New York City for work on Monday.

Trains were so crowded on the Long Island Rail Road that dozens of people missed their trains. On many early morning trains, riders couldn’t even get out the door. Others had to push their way into the cars from the platform.

There was some good news announced Monday afternoon for some commuters from New Jersey.

The Port Authority of New York and New Jersey announced that PATH trains will run between Journal Square and 33rd Street from 5 a.m. to 10 p.m. seven days a week, beginning Tuesday morning. Trains will not stop at Christopher Street or 9th Street.

While the Metropolitan Transportation Authority continues to restore service on subway and commuter rail lines, officials warned that water-logged tunnels still weren’t ready for Monday’s rush hour and that fewer-than-normal trains were running — a recipe for a difficult commute.

“Service will not be normal tomorrow, and we need you to understand that before you enter the system,” Gov. Andrew Cuomo said Sunday. “Because of the gas problem, you will have many more people on mass transit.”

Repair crews have been working around-the-clock to get mass transit back up and running after superstorm Sandy crippled much of the system.

“We are in uncharted territory with bringing this system back because of the amount of damage and saltwater in our system,” MTA Chairman Joseph Lhota said Sunday. “It’s an old system — and it’s just had a major accident.”

Additional subway trains started rolling as of midnight. The E train is now making stops from Jamaica Center to the World Trade Center and the 1 train is making stops at Chambers Street. The C train is now running all the way to its end at Euclid Avenue.

There is still no service on the B, G and Z lines. The A line is running, but service is limited.

The MTA planned to take the unusual step of using flatbed trucks to deliver 20 subway cars to the hard-hit Far Rockaway section of Queens and set up a temporary shuttle line.

The MTA warned riders it could be 10 minutes in between trains and some stations could be bypassed.

Meanwhile, citing the “substantial restoration of citywide MTA bus and subway service,” the Taxi and Limousine Commission said that it was rescinding the emergency measure that allowed taxis to pick up multiple passengers and black cars to accept street hails as of midnight tonight.

The LIRR is operating on a modified weekday schedule on all branches except the Long Beach branch on Monday.

Trains on the Ronkonkoma branch will not operate east of Ronkonkoma and trains on the Montauk Branch will not operate east of Speonk.

The LIRR is providing hourly train service between Jamaica and Atlantic Terminal/Brooklyn. Customers can walk across Atlantic Avenue to Barclays Center and connect to shuttle buses to midtown Manhattan.

Off-peak fares were in effect Monday and the on board penalty fare was waived. October monthly tickets remained valid for travel through Monday.

Metro-North Railroad trains were the sweet sound of normalcy returning to Westchester County this morning, where commuters in Katonah were happy to have at least that part of their routines back in order.

“Slowly, but it’s a lot better than it was last week, absolutely,” one rider told WCBS 880 reporter John Metaxas.

For many, it’s been seven days and nights in the cold and dark. Many huddled by their fireplaces, but one man said he had no complaints, for it could have been a lot worse.

Metro-North says train service on the Wassaic branch of the Harlem line has resumed. Regular scheduled service is also in effect between Southeast and Grand Central Terminal.

On the New Haven Line, train service has resumed on the Danbury and Waterbury Branches. The New Canaan Branch will have bus service in effect, with buses leaving stations 20 minutes before the scheduled train time.

Regularly scheduled service is in effect between New Haven/Stamford and Grand Central Terminal.

For commuters in New Jersey, NJ TRANSIT is operating only a fraction of rush hour trains to Penn Station. Emergency bus service is running from several towns to Lower Manhattan.

“There needs to be more than one bus at a time,” South Orange resident Jerry Tuttle told Hennessey Monday evening at the Port Authority bus terminal. “This is the third bus we’re waiting for.”

Buses across the state are taking residents to ferry and light rail stations.

“It took me four hours this morning to get from South Orange to my office,” commuter Dana Wade said.

“I typically take the PATH which tends to be a little bit more reliable. This morning, it took me two and half hours to get to to lower Manhattan,” said Union City resident Alaina Smith.

More than half of the system’s rails are out of commission. Boats are on tracks, bridges were destroyed, trees remain blocking some trains and foundations may be undermined.

A crew repairs tracks in Sayreville said they have been hard at work for a week, but cautioned there is no quick fix for this level of damage.

“Not at all. Not by any means nd this is just one railroad. You’ve got all the other lines that have problems too. Trees down and everything else,” NJ TRANSIT worker Frank Attardi told Hennessey.

New Jersey officials said they have requested and will be getting 350 buses from the federal government to help with the transportation issues.

“We’ve come a long way within a week and we still have a long way to go,” NJ TRANSIT spokesmand John Durso told Hennessey

Durso admitted the buses are not yet reaching everyone.

“We hear them. We’re working as hard as we can to restore service and we are. And we will get there,” Durso told Hennessey.

Early Monday morning, New Jersey Coast Line service was suspended due to overcrowding. Customers were urged to drive to Metropark for bus shuttle service to access Hoboken, Midtown and Lower Manhattan.

There is still no estimate on when all service across the Tri-State area will be restored.

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